The possible factors involved in the generation of p49a,f TaqI Y-chromosome spatial diversity in Egypt were explored. The object was to consider explanations beyond those that emphasize gene flow mediated via military campaigns within the Nile corridor during the dynastic period. Current patterns of the most common variants (V, XI, and IV) have been suggested to be primarily related to Middle Kingdom and New Kingdom political actions in Nubia, including occasional settler colonization, and the conquest of Egypt by Kush (in upper Nubia, northern Sudan), thus initiating the Twenty-Fifth Dynasty. However, a synthesis of evidence from archaeology, historical linguistics, texts, distribution of haplotypes outside Egypt, and some demographic considerations lends greater support to the establishment, before the Middle Kingdom, of the observed distributions of the most prevalent haplotypes V, XI, and IV. It is suggested that the pattern of diversity for these variants in the Egyptian Nile Valley was largely the product of population events that occurred in the late Pleistocene to mid-Holocene through the First Dynasty, and was sustained by continuous smaller-scale bidirectional migrations/interactions. The higher frequency of V in Ethiopia than in Nubia or upper (southern) Egypt has to be taken into account in any discussion of variation in the Nile Valley. Am. J. Hum. Biol. 17: 559–567, 2005. © 2005 Wiley-Liss, Inc.